BN2015 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 3.7598e-05 4.8242e-02
Layer 4 6.1831e-05 6.9902e-04
Layer 5 1.7073e-04 1.7179e-03
Layer 6 3.9921e-04 2.7774e-03
Layer 2 3.8596e-02 1.4653e-01
Layer 1 2.5588e-01 3.6894e-01
WM 9.4704e-01 3.8236e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 6 2.5146 0.7731
GAP43 Layer 5 2.6191 0.7620
STMN2 Layer 5 2.7598 0.7602
DNAJC6 Layer 5 2.3438 0.7563
EEF1A2 Layer 4 2.4668 0.7500
STXBP1 Layer 4 2.5508 0.7431
HINT1 Layer 5 2.3496 0.7387
DCLK1 Layer 4 2.6191 0.7381
ENO2 Layer 4 2.5215 0.7346
MTCH1 Layer 5 2.4395 0.7337
FXYD6 Layer 5 2.4941 0.7313
CAMK2G Layer 4 2.4453 0.7295
NAPB Layer 6 2.4395 0.7276
FBXL16 Layer 6 2.3965 0.7274
STMN1 Layer 4 2.2461 0.7270
TUBB Layer 5 2.3652 0.7270
AP2M1 Layer 5 2.4297 0.7251
SYT4 Layer 5 2.3926 0.7251
ARL6IP1 Layer 5 2.4668 0.7250
STMN3 Layer 4 2.5176 0.7249
RTN1 Layer 5 2.4844 0.7241
BASP1 Layer 5 2.2871 0.7238
ATP6V1E1 Layer 5 2.4727 0.7237
SYN2 Layer 5 2.5059 0.7221
PRKAR1A Layer 4 2.5664 0.7218
TUBB2A Layer 5 2.6426 0.7214
KLC1 Layer 5 2.4297 0.7203
CLSTN1 Layer 4 2.4668 0.7191
PI4KA Layer 6 2.4297 0.7185
TAGLN3 Layer 5 2.3867 0.7172
YWHAB Layer 4 2.4844 0.7164
RGS4 Layer 5 2.3711 0.7163
APP Layer 5 2.2520 0.7157
INPP5F Layer 4 2.7715 0.7150
ATP5F1A Layer 4 2.5176 0.7149
SNRPN Layer 4 2.4668 0.7149
STX1A Layer 5 2.4785 0.7148
GNAO1 Layer 6 2.4336 0.7140
BEX1 Layer 6 2.2871 0.7137
PRKAR1B Layer 4 2.5723 0.7133
NSF Layer 5 2.4883 0.7128
MDH1 Layer 4 2.3730 0.7127
CPLX1 Layer 4 2.4180 0.7126
MLLT11 Layer 5 2.3594 0.7121
ATP6V1A Layer 5 2.4844 0.7121
RAC1 Layer 6 2.2920 0.7118
YWHAG Layer 4 2.4844 0.7111
RAB3A Layer 4 2.4287 0.7106
BEX3 Layer 4 2.4609 0.7098
ATP1B1 Layer 4 2.4814 0.7096

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN2015
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN2015_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN2015/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN2015/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN2015/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN2015/report/PD/BN2015_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN2015/report/PD/BN2015_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 10:50:45
  • Number of Processes: 10
  • Spending Time: 0h 5m